BMRB Entry 18229

Name: NMR structure of the complex between the PH domain of the Tfb1 subunit from TFIIH and Rad2
Published: 2012-03-02

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PDB ID: 2lox
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR18229
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR structure of the complex between the PH domain of the Tfb1 subunit from TFIIH and Rad2

Deposition date:

2012-01-27

Original release date:

2012-03-02

Authors:

Lafrance-Vanasse, Julien; Legault, Pascale; Omichinski, James G.

Citation:

Citation: Lafrance-Vanasse, Julien; Arseneault, Genevieve; Cappadocia, Laurent; Chen, Hung-Ta; Legault, Pascale; Omichinski, James. "Structural and functional characterization of interactions involving the Tfb1 subunit of TFIIH and the NER factor Rad2." Nucleic Acids Res. 40, 5739-5750 (2012).
PubMed: 22373916

Assembly members:

Assembly members:
Tfb1, polymer, 119 residues, 12903.807 Da.
Rad2, polymer, 52 residues, 2279.496 Da.

Natural source:

Natural source: Common Name: baker's yeast Taxonomy ID: 4932 Superkingdom: Eukaryota Kingdom: Fungi Genus/species: Saccharomyces cerevisiae

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pGEX-2TK

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Tfb1: PSHSGAAIFEKVSGIIAINE DVSPAELTWRSTDGDKVHTV VLSTIDKLQATPASSEKMML RLIGKVDESKKRKDNEGNEV VPKPQRHMFSFNNRTVMDNI KMTLQQIISRYKDADGNSS
Rad2: GSEILERESEKESSNDENKD DDLEVLSEELFEDVPTKSQI SKEAEDNDSRKY

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	690
15N chemical shifts	173
1H chemical shifts	1092

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Tfb1	1
2	Rad2	2

Entities:

Entity 1, Tfb1 119 residues - 12903.807 Da.

1

PRO

SER

HIS

SER

GLY

ALA

ILE

PHE

GLU

2

LYS

VAL

SER

GLY

ILE

ALA

ILE

ASN

GLU

3

ASP

VAL

SER

PRO

ALA

GLU

LEU

THR

TRP

ARG

4

SER

THR

ASP

GLY

ASP

LYS

VAL

HIS

THR

VAL

5

VAL

LEU

SER

THR

ILE

ASP

LYS

LEU

GLN

ALA

6

THR

PRO

ALA

SER

GLU

LYS

MET

LEU

7

ARG

LEU

ILE

GLY

LYS

VAL

ASP

GLU

SER

LYS

8

LYS

ARG

LYS

ASP

ASN

GLU

GLY

ASN

GLU

VAL

9

VAL

PRO

LYS

PRO

GLN

ARG

HIS

MET

PHE

SER

10

PHE

ASN

ARG

THR

VAL

MET

ASP

ASN

ILE

11

LYS

MET

THR

LEU

GLN

ILE

SER

ARG

12

TYR

LYS

ASP

ALA

ASP

GLY

ASN

SER

Entity 2, Rad2 52 residues - 2279.496 Da.

1

GLY

SER

GLU

ILE

LEU

GLU

ARG

GLU

SER

GLU

2

LYS

GLU

SER

ASN

ASP

GLU

ASN

LYS

ASP

3

ASP

LEU

GLU

VAL

LEU

SER

GLU

LEU

4

PHE

GLU

ASP

VAL

PRO

THR

LYS

SER

GLN

ILE

5

SER

LYS

GLU

ALA

GLU

ASP

ASN

ASP

SER

ARG

6

LYS

TYR

Samples:

sample_1: Tfb1, [U-100% 13C; U-100% 15N], 1 mM; Rad2 1.25 mM; sodium phosphate 20 mM; EDTA 1 mM; DTT 1 mM; H2O 90%; D2O 10%

sample_2: Tfb1, [U-100% 13C; U-100% 15N], 1 mM; Rad2 1.25 mM; sodium phosphate 20 mM; EDTA 1 mM; DTT 1 mM; D2O 100%

sample_3: Tfb1, [U-100% 15N], 1 mM; Rad2 1.25 mM; sodium phosphate 20 mM; EDTA 1 mM; DTT 1 mM; H2O 90%; D2O 10%

sample_4: Tfb1 1.25 mM; Rad2, [U-100% 13C; U-100% 15N], 1 mM; sodium phosphate 20 mM; EDTA 1 mM; DTT 1 mM; H2O 90%; D2O 10%

sample_5: Tfb1 1.25 mM; Rad2, [U-100% 13C; U-100% 15N], 1 mM; sodium phosphate 20 mM; EDTA 1 mM; DTT 1 mM; D2O 100%

sample_6: Tfb1 1.25 mM; Rad2, [U-100% 15N], 1 mM; sodium phosphate 20 mM; EDTA 1 mM; DTT 1 mM; H2O 90%; D2O 10%

sample_conditions_1: pH: 6.5; pressure: 1 atm; temperature: 300 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_3	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-COSY	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_3	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_6	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_5	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_4	isotropic	sample_conditions_1
3D HNCO	sample_4	isotropic	sample_conditions_1
3D HNCACB	sample_4	isotropic	sample_conditions_1
3D H(CCO)NH	sample_4	isotropic	sample_conditions_1
3D HCCH-COSY	sample_5	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_6	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_5	isotropic	sample_conditions_1

Software:

CcpNMR v2.1, CCPN - chemical shift assignment, data analysis, peak picking

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - data analysis

NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - data analysis

NMRView, Johnson, One Moon Scientific - data analysis

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution

VNMR, Varian - collection

TALOS, Cornilescu, Delaglio and Bax - data analysis

VNMRJ, Varian - collection

NMR spectrometers:

Varian INOVA 800 MHz
Varian INOVA 600 MHz
Varian INOVA 500 MHz

BMRB	18842 19791 25540
PDB	1Y5O 2GS0 2K2U 2L2I 2LOX 2M14 2MKR 2N0Y 2LOX
DBJ	GAA22531
EMBL	CAY78811
GB	AAA35143 AAB64747 AAU09707 AHY75284 AJP38011
REF	NP_010597
SP	P32776
TPG	DAA12150
AlphaFold	P32776